*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
FILE* out;
int igrp;
real d, dd, lo, hi;
- int* ind_grp;
const char * xfn, *nfn;
- char* gn_grp;
matrix box;
gmx_bool bFreeze;
rvec dx, *x = nullptr, *v = nullptr;
{
return 0;
}
+ output_env_done(oenv);
bFreeze = opt2bSet("-of", NFILE, fnm) || opt2parg_bSet("-freeze", asize(pa), pa);
bDisre = bDisre || opt2parg_bSet("-disre_dist", npargs, pa);
const char* title = "";
bool haveTopology = false;
+ gmx_mtop_t mtop;
+ int* indexGroups = nullptr;
+ char* indexGroupNames = nullptr;
+
if (xfn != nullptr)
{
fprintf(stderr, "\nReading structure file\n");
- gmx_mtop_t mtop;
readConfAndTopology(xfn, &haveTopology, &mtop, nullptr, &x, &v, box);
title = *mtop.name;
atoms = gmx_mtop_global_atoms(&mtop);
else if ((bDisre || bConstr) && x)
{
printf("Select group to generate %s matrix from\n", bConstr ? "constraint" : "distance restraint");
- get_index(&atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
+ get_index(&atoms, nfn, 1, &igrp, &indexGroups, &indexGroupNames);
out = ftp2FILE(efITP, NFILE, fnm, "w");
if (bConstr)
{
- fprintf(out, "; constraints for %s of %s\n\n", gn_grp, title);
+ fprintf(out, "; constraints for %s of %s\n\n", indexGroupNames, title);
fprintf(out, "[ constraints ]\n");
fprintf(out, ";%4s %5s %1s %10s\n", "i", "j", "tp", "dist");
}
else
{
- fprintf(out, "; distance restraints for %s of %s\n\n", gn_grp, title);
+ fprintf(out, "; distance restraints for %s of %s\n\n", indexGroupNames, title);
fprintf(out, "[ distance_restraints ]\n");
fprintf(out, ";%4s %5s %1s %5s %10s %10s %10s %10s %10s\n", "i", "j", "?", "label",
"funct", "lo", "up1", "up2", "weight");
{
for (j = i + 1; j < igrp; j++, k++)
{
- rvec_sub(x[ind_grp[i]], x[ind_grp[j]], dx);
+ rvec_sub(x[indexGroups[i]], x[indexGroups[j]], dx);
d = norm(dx);
if (bConstr)
{
- fprintf(out, "%5d %5d %1d %10g\n", ind_grp[i] + 1, ind_grp[j] + 1, 2, d);
+ fprintf(out, "%5d %5d %1d %10g\n", indexGroups[i] + 1, indexGroups[j] + 1, 2, d);
}
else
{
}
lo = std::max(0.0_real, d - dd);
hi = d + dd;
- fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n", ind_grp[i] + 1,
- ind_grp[j] + 1, 1, k, 1, lo, hi, hi + disre_up2, 1.0);
+ fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n", indexGroups[i] + 1,
+ indexGroups[j] + 1, 1, k, 1, lo, hi, hi + disre_up2, 1.0);
}
}
}
else
{
printf("Select group to position restrain\n");
- get_index(&atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
+ get_index(&atoms, nfn, 1, &igrp, &indexGroups, &indexGroupNames);
out = ftp2FILE(efITP, NFILE, fnm, "w");
- fprintf(out, "; position restraints for %s of %s\n\n", gn_grp, title);
+ fprintf(out, "; position restraints for %s of %s\n\n", indexGroupNames, title);
fprintf(out, "[ position_restraints ]\n");
fprintf(out, ";%3s %5s %9s %10s %10s\n", "i", "funct", "fcx", "fcy", "fcz");
for (i = 0; i < igrp; i++)
{
- fprintf(out, "%4d %4d %10g %10g %10g\n", ind_grp[i] + 1, 1, fc[XX], fc[YY], fc[ZZ]);
+ fprintf(out, "%4d %4d %10g %10g %10g\n", indexGroups[i] + 1, 1, fc[XX], fc[YY], fc[ZZ]);
}
gmx_ffclose(out);
}
sfree(v);
done_atom(&atoms);
}
+ sfree(indexGroupNames);
+ sfree(indexGroups);
return 0;
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for gmx genrestr.
+ *
+ * \author Kevin Boyd <kevin44boyd@gmail.com>
+ */
+
+#include "gmxpre.h"
+
+#include "gromacs/gmxpreprocess/genrestr.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/filematchers.h"
+#include "testutils/refdata.h"
+#include "testutils/stdiohelper.h"
+#include "testutils/testfilemanager.h"
+#include "testutils/textblockmatchers.h"
+
+namespace gmx
+{
+namespace test
+{
+
+class GenRestrTest : public CommandLineTestBase
+{
+public:
+ void runTest(const std::string& interactiveCommandLineInput)
+ {
+ StdioTestHelper stdIoHelper(&fileManager());
+ stdIoHelper.redirectStringToStdin(interactiveCommandLineInput.c_str());
+
+ CommandLine& cmdline = commandLine();
+ // Provide the name of the module to call
+ std::string module[] = { "genrestr" };
+ cmdline.merge(CommandLine(module));
+
+ ASSERT_EQ(0, gmx_genrestr(cmdline.argc(), cmdline.argv()));
+ checkOutputFiles();
+ }
+};
+
+TEST_F(GenRestrTest, SimpleRestraintsGenerated)
+{
+ setInputFile("-f", "lysozyme.pdb");
+ ExactTextMatch settings;
+ setOutputFile("-o", "restraints.itp", TextFileMatch(settings));
+ // Select c-alphas from default index options.
+ std::string selection = "3";
+ runTest(selection);
+}
+} // namespace test
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff